scgpt 0.1.3

Large-scale generative pretrain of single cell using transformer.

scGPT

This is the official codebase for scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI.

Preprint

Documentation

!UPDATE: We have released several new pretrained scGPT checkpoints. Please see the Pretrained scGPT checkpoints section for more details.

Installation

scGPT works with Python >= 3.7 and R >=3.6.1. Please make sure you have the correct version of Python and R installed pre-installation.

scGPT is available on PyPI. To install scGPT, run the following command:

$ pip install scgpt

[Optional] We recommend using wandb for logging and visualization.

$ pip install wandb

For developing, we are using the Poetry package manager. To install Poetry, follow the instructions here.

$ git clone this-repo-url
$ cd scGPT
$ poetry install

Note: The flash-attn dependency usually requires specific GPU and CUDA version. If you encounter any issues, please refer to the flash-attn repository for installation instructions. For now, May 2023, we recommend using CUDA 11.7 and flash-attn<1.0.5 due to various issues reported about installing new versions of flash-attn.

Pretrained scGPT Model Zoo

Here is the list of pretrained models. Please find the links for downloading the checkpoint folders. We recommend using the whole-human model for most applications by default. If your fine-tuning dataset shares similar cell type context with the training data of the organ-specific models, these models can usually demonstrate competitive performance as well.

Model name	Description	Download
whole-human (recommended)	Pretrained on 33 million normal human cells.	link
brain	Pretrained on 13.2 million brain cells.	link
blood	Pretrained on 10.3 million blood and bone marrow cells.	link
heart	Pretrained on 1.8 million heart cells	link
lung	Pretrained on 2.1 million lung cells	link
kidney	Pretrained on 814 thousand kidney cells	link
pan-cancer	Pretrained on 5.7 million cells of various cancer types	link

Fine-tune scGPT for scRNA-seq integration

Please see our example code in examples/finetune_integration.py. By default, the script assumes the scGPT checkpoint folder stored in the examples/save directory.

To-do-list

• Upload the pretrained model checkpoint
• Publish to pypi
• Provide the pretraining code with generative attention masking
• Finetuning examples for multi-omics integration, cell type annotation, perturbation prediction, cell generation
• Example code for Gene Regulatory Network analysis
• Documentation website with readthedocs
• Bump up to pytorch 2.0
• New pretraining on larger datasets
• Reference mapping example
• Publish to huggingface model hub

Contributing

We greatly welcome contributions to scGPT. Please submit a pull request if you have any ideas or bug fixes. We also welcome any issues you encounter while using scGPT.

Acknowledgements

We sincerely thank the authors of following open-source projects:

• flash-attention
• scanpy
• scvi-tools
• scib
• datasets
• transformers

Citing scGPT

@article{cui2023scGPT,
title={scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI},
author={Cui, Haotian and Wang, Chloe and Maan, Hassaan and Pang, Kuan and Luo, Fengning and Wang, Bo},
journal={bioRxiv},
year={2023},
publisher={Cold Spring Harbor Laboratory}
}